Nodulin gene expression in effective alfalfa nodules and in nodules arrested at three different stages of development

Early nodulin genes are induced in alfalfa root outgrowths elicited by auxin transport inhibitors

Rhizobium nod genes are essential for root hair deformation and cortical cell division, early stages in the development of nitrogen-fixing root nodules. Nod(-) mutants are unable to initiate nodules on legume roots. We observed that N-(1-naphthyl)phthalamic acid and 2,3,5-triiodobenzoic acid, compounds known to function as auxin transport inhibitors, induced nodule-like structures on alfalfa roots. The nodule-like structures (pseudonodules) were white, devoid of bacteria, and resembled nodules elicited by Rhizobium meliloti exopolysaccharide (exo) mutants at both the histological and molecular level. Two nodulin genes, ENOD2 and Nms-30, were expressed. RNA isolated from the nodule-like structures hybridized to pGmENOD2, a soybean early nodulin cDNA clone. RNA isolated from roots did not hybridize. We determined by in vitro translations of total RNA that the alfalfa nodulin transcript Nms-30 was also expressed in the nodule-like structures. The late expressed nodulin genes, such as the leghemoglobin genes, were not transcribed. Because N-(1-naphthyl)phthalamic acid and 2,3,5-triiodobenzoic acid induce the development of nodules on alfalfa roots, we suggest that the auxin transport inhibitors mimic the activity of compound(s) made upon the induction of the Rhizobium nod genes.

Differentiation of symbiotic cells and endosymbionts in Medicago truncatula nodulation are coupled to two transcriptome-switches

The legume plant Medicago truncatula establishes a symbiosis with the nitrogen-fixing bacterium Sinorhizobium meliloti which takes place in root nodules. The formation of nodules employs a complex developmental program involving organogenesis, specific cellular differentiation of the host cells and the endosymbiotic bacteria, called bacteroids, as well as the specific activation of a large number of plant genes. By using a collection of plant and bacterial mutants inducing non-functional, Fix(-) nodules, we studied the differentiation processes of the symbiotic partners together with the nodule transcriptome, with the aim of unravelling links between cell differentiation and transcriptome activation. Two waves of transcriptional reprogramming involving the repression and the massive induction of hundreds of genes were observed during wild-type nodule formation. The dominant features of this "nodule-specific transcriptome" were the repression of plant defense-related genes, the transient activation of cell cycle and protein synthesis genes at the early stage of nodule development and the activation of the secretory pathway along with a large number of transmembrane and secretory proteins or peptides throughout organogenesis. The fifteen plant and bacterial mutants that were analyzed fell into four major categories. Members of the first category of mutants formed non-functional nodules although they had differentiated nodule cells and bacteroids. This group passed the two transcriptome switch-points similarly to the wild type. The second category, which formed nodules in which the plant cells were differentiated and infected but the bacteroids did not differentiate, passed the first transcriptome switch but not the second one. Nodules in the third category contained infection threads but were devoid of differentiated symbiotic cells and displayed a root-like transcriptome. Nodules in the fourth category were free of bacteria, devoid of differentiated symbiotic cells and also displayed a root-like transcriptome. A correlation thus exists between the differentiation of symbiotic nodule cells and the first wave of nodule specific gene activation and between differentiation of rhizobia to bacteroids and the second transcriptome wave in nodules. The differentiation of symbiotic cells and of bacteroids may therefore constitute signals for the execution of these transcriptome-switches.

The ribosomal protein P0 of soybean (Glycine max L. Merr.) has antigenic cross-reactivity to soybean seed lectin

Soybean (Glycine max L. Merr.) mutants lacking the ability to produce the lectin normally found in soybean seeds (SBL) are designated Le-. A protein of higher molecular weight that cross-reacts with antibodies raised to SBL was found at nearly equivalent levels in roots, hypocotyls, and leaves, and at lower levels in cotyledons and dry seeds of both Le+ and Le- soybean cultivars. Earlier work suggested that this protein was a novel lectin. Clones isolated from a Le- soybean root cDNA library produced a cross-reacting protein of the same size in Escherichia coli. Sequence analysis of these clones revealed a high degree of similarity to the ribosomal protein P0. The cross-reacting protein co-purified with ribosomes, and a monoclonal antibody raised to purified brine shrimp P0 cross-reacted to the same protein. The protein showed no lectin activity in a hemagglutination assay, nor did it bind to an N-acetyl-D-galactosamine affinity column. On the basis of this evidence, we conclude that the SBL-cross-reacting protein is not a lectin but a homologue of the ribosomal protein P0. Consequently, Le- soybeans must produce a lectin that is dissimilar to SBL at both the DNA and amino acid levels and we suggest that it is this lectin which is involved in nodulation.

Rhizobium meliloti exopolysaccharides: synthesis and symbiotic function

Bacterial exopolysaccharide (EPS) is required for establishment of the nitrogen-fixing symbiosis between Rhizobium meliloti and its host plant, Medicago sativa (alfalfa), but the precise role of EPS in this interaction is not well defined. Bacterial mutants which fail to produce EPS induce nodules on the roots of the host plant, but fail to invade these root nodules. Research conducted in our lab and others suggests that EPS plays a specific role in the R. meliloti-M. sativa symbiosis. A common theme emerging from these studies is that small quantities of low-molecular-weight (LMW) EPS are sufficient to mediate successful invasion by R. meliloti mutants which fail to produce EPS, implying that LMW EPS may act as a signaling molecule during this process.

Expression of nodulin genes in plant-determined ineffective nodules of pea

The mutant E135 (sym 13) of pea (Pisum sativum L.) forms a normal number of small white nodules that contain bacteroids, but these bacteroids lack nitrogenase activity. To evaluate the effects of the sym 13 gene on the expression of nodulin genes, cDNA clones for nodulins were isolated from pea nodules and the expression of nodulin genes in ineffective E135 nodules was compared with that in nitrogen-fixing nodules on the wild-type parent, cv. Sparkle. Nineteen cDNA clones for nodulins, including ENOD2 and cDNAs for two distinct leghemoglobins (Lbs), were isolated from Sparkle nodules by a subtractive hybridization procedure. All the nodulin genes examined were expressed in nodules on both E135 and Sparkle plants. However, the level of expression of seven genes, one of which was an Lb gene that corresponded to PsN5, was significantly lower in E135 nodules. The levels of Lb apo-proteins, with the exception of Lb-III and Lb-IV, in E135 nodules resembled those in Sparkle nodules, but the level of heme in E135 nodules was lower than that in Sparkle nodules. Although the expression of the two Lb genes that corresponded to PsN5 and PsN120 in E135 nodules was slightly depressed by exogenous ammonia, the level of the PsN5 transcript was still lower than the control level in Sparkle nodules. Our results indicate that the plant gene sym 13 does not influence the induction of nodulin genes but does influence the level of the expression of some genes, one of which is a gene for Lb, as well as the level of heme.

Five Nodulation Mutants of White Sweetclover (Melilotus alba Desr.) Exhibit Distinct Phenotypes Blocked at Root Hair Curling, Infection Thread Development, and Nodule Organogenesis

In an effort to obtain a developmental sequence of mutations in the Rhizobium-legume interaction within a single legume species, we have characterized the early events of nodule development in 10 nodulation mutants of sweetclover, Melilotus alba Desr. cv U389, representing five genetic loci. Both seed and root exudates from all of the sweetclover mutants induced expression of the nod genes of Rhizobium meliloti. Mutants in three loci were blocked in the early stages of root hair curling. Of these, a mutant in the sym-3 locus exhibited root hair deformations in response to inoculation with R. meliloti but produced no nodules or emerging nodule primordia, suggesting a blockage in the signal transduction events leading to nodule organogenesis. In contrast, mutants in both the sym-1 and sym-5 loci formed ineffective nodules in response to inoculation but differed slightly in the type of root hair response observed. None of these three early mutants formed infection threads. Infection threads were observed in mutant sym-2 as well as in ineffective nodules. Mutant sym-4 also formed infection threads but lacked nodules. The phenotypes observed for mutants from these five loci suggest that a secondary receptor or signal produced by the plant is required for nodule development.

Differential expression within the glutamine synthetase gene family of the model legume Medicago truncatula

The glutamine synthetase (GS) gene family of Medicago truncatula Gaertn. contains three genes related to cytosolic GS (MtGSa, MtGSb, and MtGSc), although one of these (MtGSc) appears not to be expressed. Sequence analysis suggests that the genes are more highly conserved interspecifically rather than intraspecifically: MtGSa and MtGSb are more similar to their homologs in Medicago sativa and Pisum sativum than to each other. Studies in which gene-specific probes are used show that both MtGSa and MtGSb are induced during symbiotic root nodule development, although not coordinately. MtGSa is the most highly expressed GS gene in nodules but is also expressed to lower extents in a variety of other organs. MtGSb shows higher levels of expression in roots and the photosynthetic cotyledons of seedlings than in nodules or other organs. In roots, both genes are expressed in the absence of an exogenous nitrogen source. However the addition of nitrate leads to a short-term, 2- to 3-fold increase in the abundance of both mRNAs, and the addition of ammonium leads to a 2-fold increase in MtGSb mRNA. The nitrogen supply, therefore, influences the expression of the two genes in roots, but it is clearly not the major effector of their expression. In the discussion section, the expression of the GS gene family of the model legume M. truncatula is compared to those of other leguminous plants.

A Rhizobium meliloti homolog of the Escherichia coli peptide-antibiotic transport protein SbmA is essential for bacteroid development

Alfalfa nodules induced by a Rhizobium meliloti strain carrying the bacA386::TnphoA mutation (formerly fix386::TnphoA) were examined by light and electron microscopy. These ineffective nodules were found to contain bacteria within infection threads, but no mature bacteroids were observed. A closer examination revealed that there were undeveloped senescent bacteroids in the plant cells of the nodule invasion zone, strongly suggesting that the symbiotic defect of the bacA386::TnphoA mutant is attributable to an early block in bacteroid development. The expression of the bacA gene in effective nodules was monitored with a bacA-phoA fusion and found to be strongest in the region where developing bacteroids are found. The bacA+ gene was cloned and sequenced. Sequence analysis indicated that BacA is probably an integral inner membrane protein with seven transmembrane domains and that it is extremely homologous to Escherichia coli SbmA, an inner membrane protein required for the uptake of microcin B17, a peptide antibiotic. Southern blotting experiments indicate that a gene closely related to bacA/sbmA is found in many bacteria, including some that invade eukaryotic cells. Possible roles for BacA in symbiosis are discussed.

The PsENOD12 Gene Is Expressed at Two Different Sites in Afghanistan Pea Pseudonodules Induced by Auxin Transport Inhibitors

A number of early nodulin genes are expressed in specific cell types as pea (Pisum sativum) root nodules develop. The Pisum sativum early nodulin PsENOD2 is detected only in the uninfected cells of the nodule parenchyma, whereas PsENOD12 is expressed at two spatially removed sites: in root hairs and adjacent cortical cells, both of which can be invaded by Rhizobium entering through infection threads, and in derivatives of newly divided root inner cortical cells that establish the nodule primordium. We tested whether Rhizobium infection is required for triggering PsENOD12 gene expression by inducing nodule-like structures on Afghanistan pea roots with the auxin transport inhibitor N-(1-naphthyl)phthalamic acid (NPA). These nodule-like structures lack infection threads but resemble Rhizobium-induced nodules in other aspects. For one, both PsENOD2 and PsENOD12 transcripts were detected in these structures. PsENOD2 mRNA was localized by in situ hybridization to a zone equivalent to the nodule parenchyma of Rhizobium-induced nodules, whereas PsENOD12 transcripts were detected in a group of cells comparable to the nodule primordium of developing nodules. In addition, PsENOD12 mRNA was detected in uninfected root hairs 48 h after NPA treatment. These results indicate that infection is not a trigger for PsENOD12 gene expression in Afghanistan pea and rather suggest that the expression of the PsENOD2 and PsENOD12 genes is correlated with the differentiation of specific cell types in the developing nodule.

Aspartate aminotransferase in effective and ineffective alfalfa nodules : cloning of a cDNA and determination of enzyme activity, protein, and mRNA levels

Aspartate aminotransferase (AAT) is a key plant enzyme affecting nitrogen and carbon metabolism, particularly in legume root nodules and leaves of C(4) species. To ascertain the molecular genetic characteristics and biochemical regulation of AAT, we have isolated a cDNA encoding the nodule-enhanced AAT (AAT-2) of alfalfa (Medicago sativa L.) by screening a root nodule cDNA expression library with antibodies. Complementation of an Escherichia coli AAT mutant with the alfalfa nodule AAT-2 cDNA verified the identity of the clone. The deduced amino acid sequence of alfalfa AAT-2 is 53 and 47% identical to animal mitochondrial and cytosolic AATs, respectively. The deduced molecular mass of AAT-2 is 50,959 daltons, whereas the mass of purified AAT-2 is about 40 kilodaltons as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the protein's N-terminal domain (amino acids 1-59) contains many of the characteristics of plastid-targeting peptides. We postulate that AAT-2 is localized to the plastid. Southern blot analysis suggests that AAT-2 is encoded by a small, multigene family. The expression of AAT-2 mRNA in nodules is severalfold greater than that in either leaves or roots. Northern and western blots showed that expression of AAT activity during effective nodule development is accompanied by a sevenfold increase in AAT-2 mRNA and a comparable increase in enzyme protein. By contrast, plant-controlled ineffective nodules express AAT-2 mRNA at much lower levels and have little to no AAT-2 enzyme protein. Expression of root nodule AAT-2 appears to be regulated by at least two events: the first is independent of nitrogenase activity; the second is associated with nodule effectiveness.

Suppression of the ndv mutant phenotype of Rhizobium meliloti by cloned exo genes

The ndvA and ndvB genes of Rhizobium meliloti are involved in the export and synthesis, respectively, of the small cyclic polysaccharide beta(1,2)glucan. We have previously shown that spontaneous symbiotic pseudorevertants of ndv mutants do not produce periplasmic beta(1,2)glucan. Here we show that the pseudorevertants also do not produce extracellular beta(1,2)glucan, but do show alterations in the amount of the major acidic exopolysaccharide produced. This exopolysaccharide is not detectably different from that produced by the wild type or by the ndv mutants. A cosmid which suppresses the symbiotic defect of both ndvA and ndvB mutants was isolated from a gene bank prepared from DNA of an ndvA pseudorevertant. This cosmid contains a number of exo genes, including exoH and exoF. Subcloning and Tn5 mutagenesis were used to show that the widely separated exoH and exoF genes are both involved in suppression of the ndv mutant phenotype and that the 3.5 kb DNA fragment which contains the exoH gene does not carry the mutation responsible for second site suppression.

Nodules elicited by Rhizobium meliloti heme mutants are arrested at an early stage of development

Heme-deficient mutants of Rhizobium and Bradyrhizobium have been found to exhibit diverse phenotypes with respect to symbiotic interactions with plant hosts. We observed that R. meliloti hemA mutants elicit nodules that do not contain intracellular bacteria; the nodules contain either no infection threads ("empty" nodule phenotype) or aberrant infection threads that failed to release bacteria (Bar- phenotype). These mutant nodules expressed nodulin genes associated with nodules arrested at an early stage of development, including ENOD2, Nms-30, and four previously undescribed nodulin genes. These nodules also failed to express any of six late nodulin genes tested by hybridization, including leghemoglobin, and twelve tested by in vitro translation product analysis which are not yet correlated with specific cloned genes. We observed that R. meliloti leucine and adenosine auxotrophs induced invaded Fix- nodules that expressed late nodulin genes, suggesting that it is not auxotrophy per se that causes the hemA mutants to elicit Bar- or empty nodules. Because R. meliloti hemA mutants elicit nodules that do not contain intracellular bacteria, it is not possible to decide whether or not the Fix- phenotype of these nodules is a direct consequence of the failure of R. meliloti to supply the heme moiety of hololeghemoglobin. Our results demonstrate the importance of establishing the stage in development at which a mutant nodule is arrested before conclusions are drawn about the role of small metabolite exchange in the symbiosis.

The exoD gene of Rhizobium meliloti encodes a novel function needed for alfalfa nodule invasion

During the symbiotic interaction between alfalfa and the nitrogen-fixing bacterium Rhizobium meliloti, the bacterium induces the formation of nodules on the plant roots and then invades these nodules. Among the bacterial genes required for nodule invasion are the exo genes, involved in production of an extracellular polysaccharide, and the ndv genes, needed for production of a periplasmic cyclic glucan. Mutations in the exoD gene result in altered exopolysaccharide production and in a nodule invasion defect. In this work we show that the stage of symbiotic arrest of exoD mutants is similar to that of other exo and ndv mutants. However, the effects of exoD mutations on exopolysaccharide production and growth on various media are different from the effects of other exo and ndv mutations. Finally, exoD mutations behave differently from other exo mutations in their ability to be suppressed or complemented extracellularly. The results suggest that exoD represents a new class of Rhizobium genes required for nodule invasion, distinct from the other exo genes and the ndv genes. We discuss models for the function of exoD.

sym 13-A Gene Conditioning Ineffective Nodulation in Pisum sativum

Treatment of Pisum sativum (L.) cv. ;Sparkle' with ethyl methanesulfonic acid (EMS) produced a stable mutant, E135F, which forms small, white, ineffective nodules. These nodules exhibit histological zonation typical of an indeterminant nodule, e.g. meristematic, early symbiotic, late symbiotic, and senescent zones. Compared with the nitrogen fixing nodules of the parent, the zones are smaller and the nodules senesce prematurely. Bacteroids in E135F are less elongated and less differentiated than those in ;Sparkle.' The E135F mutant forms ineffective nodules when inoculated with nine different effective strains of Rhizobium leguminosarum and also when grown in a soil containing effective strains. The ineffective phenotype of E135F is under monogenic recessive control; the gene is designated sym 13. sym 13 was located on chromosome 2 by linkage with genes for shikimic dehydrogenase and esterase-2. The original selection E135F carried another mutation in heterozygous form at a separate locus, yielding some homozygous recessive nonnodulating progeny, E135N, in later generations. This indicates that EMS treatments may cause mutations at more than one sym gene. The gene conditioning non-nodulation in E135N was designated sym 14. It mapped to a locus on a different part of chromosome 2 by linkage to the gene for fumarase. The data demonstrate that sym genes are not necessarily closely linked.

Genetic analyses of Rhizobium meliloti exopolysaccharides

We have recently obtained strong genetic evidence that the acidic Calcofluor-binding exopolysaccharide (EPS I) of Rhizobium meliloti Rm1021 is required for nodule invasion and possibly for later events in nodule development. Thirteen loci on the second megaplasmid have been identified that are required for, or affect, the synthesis of EPS I. Mutations in certain of these loci completely abolish the production of EPS I and result in mutants that form empty Fix- nodules. exoH mutants fail to succinylate their EPS I and form empty Fix- nodules. We have identified two unlinked regulatory loci, exoR and exoS, whose products play negative roles in the regulation of expression of the exo genes. We have recently discovered that R. meliloti has a latent capacity to synthesize a second exopolysaccharide (EPS II) that can substitute for the role(s) of EPS I in nodulation of alfalfa but not of other hosts. Possible roles for Rhizobium exopolysaccharides in nodulation are discussed.

Modulation of Host Gene Expression during Initiation and Early Growth of Nodules in Cowpea, Vigna unguiculata (L.) Walp

Inoculation of 2-day-old cowpea (Vigna unguiculata [L.] Walp.) seedlings with Rhizobium fredii USDA257 results in proficient nodulation of the tap root. The most abundant nodulation occurs in a region roughly corresponding to the position of the root tip at the time of inoculation. We have examined plant gene expression in this region, after inoculation with either USDA257 or a nonnodulating mutant, 257B3. After isolation of mRNA and in vitro translation, the protein products were separated by two-dimensional gel electrophoresis. Seven proteins are induced within 2.5 days after inoculation with USDA257. One additional induced protein is detectable by 3.5 days after inoculation, and three more appear by day 6. Three of the proteins that are differentially expressed at 2.5 and 3.5 days after inoculation are produced at equivalent levels after 6 days, indicating transient induction of these genes during early stages of nodule development. Several proteins were more abundant in translations of mRNA from roots that had been inoculated with the nonnodulating mutant. This was particularly true after 6 days, when nine proteins were in this class. Thus, altered plant gene expression in carefully selected, highly responsive tissue can be detected 2 days before emerging nodules are visible on the roots, and 6 to 7 days before acetylene reduction is detectable. Additionally, comparisons of ionically bound cell wall proteins isolated 6 days after inoculation revealed four that were unique to nodulating roots, suggesting that some of the nodulation-induced genes may code for structural proteins.

Developmental regulation of enzymes of sucrose and hexose metabolism in effective and ineffective soybean nodules

Soybean (Glycine max) nodules formed by inoculation with either an effective strain or an ineffective (noninvasive, nodule-forming) strain of Bradyrhizobium japonicum were assayed for changes in developmental patterns of carbon metabolic enzymes of the plant nodule cells. Of the enzyme activities measured, only sucrose synthase, glutamine synthetase, and alcohol dehydrogenase were altered in the ineffective nodules relative to the effective nodules. Sucrose synthase and glutamine synthetase activities were greatly reduced, whereas alcohol dehydrogenase activity was elevated. Dark-induced senescence severely affected sucrose synthase but had little, if any, effect on the other enzymes measured. The developmental patterns of the anaerobically induced enzymes, aldolase and alcohol dehydrogenase, were different from those expected, implying that their development is not regulated solely by oxygen deprivation. However, anaerobic treatment of nodules resulted in responses similar to those enzymes in maize. The developmental profiles of the carbon metabolic enzymes suggest that carbohydrates are metabolized via the sucrose synthase and pentose phosphate pathways. This route of carbon metabolism, compared to glycolysis, would reduce the requirement of ATP for carbohydrate catabolism, generate NADPH for biosynthetic reactions, and provide intermediates for plant secondary metabolism.

Involvement of Rhizobium leguminosarum nodulation genes in gene expression in pea root hairs

The mRNA population in pea root hairs was characterized by means of in vitro translation of total root hair RNA followed by 2-dimensional gel electrophoresis of the translation products. Root hairs contain several mRNAs not detectable in total RNA preparations from roots. Most of these root hair-specific mRNAs occur in elongating root hairs at higher levels than in mature root hairs. The expression of some genes in pea root hairs is typically affected by inoculation with Rhizobium leguminosarum. One gene, encoding RH-42, is specifically induced while the expression of another gene, encoding RH-44, is markedly enhanced. Using R. leguminosarum mutants it was shown that the nodC gene is required for the induction and enhancement of expression of the RH-42 and RH-44 genes, respectively, while the Rhizobium chromosomal gene pss1, involved in exopolysaccharide synthesis, is not essential. After induction of the nod genes with apigenin the bacteria excrete into the culture medium a factor that causes root hair deformation. This deformation factor stimulates the expression of the RH-44 gene but does not induce the expression of the gene encoding RH-42.